Mercurial > repos > dfornika > kma_result_to_mlst

annotate kma_result_to_mlst.py @ 0:934f961a7189 draft default tip

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"planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/kma_result_to_mlst commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
author dfornika
date Thu, 31 Oct 2019 14:12:43 -0400
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934f961a7189 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/kma_result_to_mlst commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
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1 #!/usr/bin/env python
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2
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3 from __future__ import print_function
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4
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5 import argparse
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6 import csv
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7 import json
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8 import os
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9 import sys
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11 from pprint import pprint
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12
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13 def parse_res_file(res_file_path):
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14 LOCUS_ALLELE_DELIMITER = '_'
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15
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16 res_fieldnames = [
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17 'template',
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18 'score',
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19 'expected',
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20 'template_length',
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21 'template_identity',
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22 'template_coverage',
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23 'query_identity',
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24 'query_coverage',
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25 'depth',
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26 'q_value',
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27 'p_value',
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28 ]
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29
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30 with open(res_file_path, 'r') as f:
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31 loci = {}
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32 reader = csv.DictReader(f, fieldnames=res_fieldnames, dialect="excel-tab")
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33 next(reader) #skip header
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34 for row in reader:
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35 locus, allele = map(str.strip, row['template'].split(LOCUS_ALLELE_DELIMITER))
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36 if locus in loci:
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37 loci[locus][allele] = {
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38 'locus_id': locus,
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39 'allele_id': allele,
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40 'score': int(row['score'].strip()),
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41 'expected': int(row['expected'].strip()),
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42 'template_length': int(row['template_length'].strip()),
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43 'template_identity': float(row['template_identity'].strip()),
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44 'template_coverage': float(row['template_coverage'].strip()),
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45 'query_identity': float(row['query_identity'].strip()),
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46 'query_coverage': float(row['query_coverage'].strip()),
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47 'depth': float(row['depth'].strip()),
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48 'q_value': float(row['q_value'].strip()),
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49 'p_value': float(row['p_value'].strip()),
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50 }
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51 else:
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52 loci[locus] = {}
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53 loci[locus][allele] = {
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54 'locus_id': locus,
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55 'allele_id': allele,
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56 'score': int(row['score'].strip()),
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57 'expected': int(row['expected'].strip()),
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58 'template_length': int(row['template_length'].strip()),
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59 'template_identity': float(row['template_identity'].strip()),
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60 'template_coverage': float(row['template_coverage'].strip()),
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61 'query_identity': float(row['query_identity'].strip()),
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62 'query_coverage': float(row['query_coverage'].strip()),
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63 'depth': float(row['depth'].strip()),
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64 'q_value': float(row['q_value'].strip()),
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65 'p_value': float(row['p_value'].strip()),
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66 }
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67
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68 return loci
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69
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70 def main(args):
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71
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72 loci = parse_res_file(args.res)
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73 print("\t".join([
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74 "locus_id",
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75 "allele_id",
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76 "template_identity",
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77 "template_coverage",
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78 "depth",
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79 ]))
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80
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81 for locus, alleles in loci.items():
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82 best_allele = sorted(alleles.values(),
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83 key=lambda x: x['score'], reverse=True)[0]['allele_id']
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84
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85 print("\t".join([
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86 alleles[best_allele]['locus_id'],
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87 alleles[best_allele]['allele_id'],
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88 str(alleles[best_allele]['template_identity']),
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89 str(alleles[best_allele]['template_coverage']),
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90 str(alleles[best_allele]['depth']),
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91 ]))
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92
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93 if __name__ == '__main__':
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94 parser = argparse.ArgumentParser()
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95 parser.add_argument("--res", dest="res", help="KMA result overview file")
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96 args = parser.parse_args()
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97 main(args)